Lyme arthritis is caused by infection with the tick-borne spirochete Borrelia burgdorferi and in humans is responsible for a number of symptoms involving the heart, joints, central and peripheral nervous system, and skin. A self-limiting, acute arthritis developing one to several months following infection is reported in 60% of patients not treated at the time of the tick bite. Genetic regulation of disease severity is evident in B. burgdorferi-infected mice as C3H mice display severe arthritis while C57BL/6 (B6) mice develop mild to moderate arthritis. Localized induction of Type I IFN has been associated with severe Lyme arthritis development in C3H mice. B. burgdorferi arthritis associated (Bbaa) Quantitative Trait Loci (QTL) on five chromosomes were previously identified, and reciprocal interval specific congenic lines (ISCL) of mice have been generated and tested for penetrant arthritis phenotypes. ISCL encompassing Bbaa2Bbaa3 on chromosome 5 and Bbaa4 on chromosome 11 transferred arthritis phenotypes in both directions. Interval specific recombinant congenic lines (ISRCL) have been generated within Bbaa2Bbaa3 resulting in significantly delimiting the physical boundaries encompassing the relevant loci. Two loci have been identified with enhanced influence on arthritis phenotype; Bbaa2a at 119.18-125.31Mbp and Bbaa2b at 127.40-137.53Mbp. A third region, Bbaa2c at 125.31-127.40Mbp, suppresses phenotypes attributed to Bbaa2b. ISRCL across the Bbaa4 interval on chromosome 11 have also been generated and physical mapping of the relevant locus is anticipated. The exciting finding of increased phenotype in the narrowed ISRCL is a major advance towards the ultimate goal of identifying the allelic genes responsible for the difference in arthritis severity in B6 and C3H mice following infection with B. burgdorferi. Four approaches that incorporate genetics, molecular biology, and biological characterization are proposed for the identification of these genes: 1) high resolution congenic mapping of Bbaa2a, Bbaa2b, and Bbaa4; 2) identification of positional candidates by comparative sequence and expression analysis; 3) determine the contribution of Type I IFN to arthritis in each ISRCL; and 4) using RNA silencing to assess candidate genes for modulation of B. burgdorferi signaling in macrophages.